Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signature

Background

Non-small cell lung cancer (NSCLC) represents more than about 80% of the lung cancer. The early stages of NSCLC can be treated with complete resection with a good prognosis. However, most cases are detected at late stage of the disease. The average survival rate of the patients with invasive lung cancer is only about 4%. Adenocarcinoma in situ (AIS) is an intermediate subtype of lung adenocarcinoma that exhibits early stage growth patterns but can develop into invasion.

Methods

In this study, we used RNA-seq data from normal, AIS, and invasive lung cancer tissues to identify a gene module that represents the distinguishing characteristics of AIS as AIS-specific genes. Two differential expression analysis algorithms were employed to identify the AIS-specific genes. Then, the subset of the best performed AIS-specific genes for the early lung cancer prediction were selected by random forest. Finally, the performances of the early lung cancer prediction were assessed using random forest, support vector machine (SVM) and artificial neural networks (ANNs) on four independent early lung cancer datasets including one tumor-educated blood platelets (TEPs) dataset.

Results

Based on the differential expression analysis, 107 AIS-specific genes that consisted of 93 protein-coding genes and 14 long non-coding RNAs (lncRNAs) were identified. The significant functions associated with these genes include angiogenesis and ECM-receptor interaction, which are highly related to cancer development and contribute to the smoking-free lung cancers. Moreover, 12 of the AIS-specific lncRNAs are involved in lung cancer progression by potentially regulating the ECM-receptor interaction pathway. The feature selection by random forest identified 20 of the AIS-specific genes as early stage lung cancer signatures using the dataset obtained from The Cancer Genome Atlas (TCGA) lung adenocarcinoma samples. Of the 20 signatures, two were lncRNAs, BLACAT1 and CTD-2527I21.15 which have been reported to be associated with bladder cancer, colorectal cancer and breast cancer. In blind classification for three independent tissue sample datasets, these signature genes consistently yielded about 98% accuracy for distinguishing early stage lung cancer from normal cases. However, the prediction accuracy for the blood platelets samples was only 64.35% (sensitivity 78.1%, specificity 50.59%, and AUROC 0.747).

Conclusions

The comparison of AIS with normal and invasive tumor revealed diseases-specific genes and offered new insights into the mechanism underlying AIS progression into an invasive tumor. These genes can also serve as the signatures for early diagnosis of lung cancer with high accuracy. The expression profile of gene signatures identified from tissue cancer samples yielded remarkable early cancer prediction for tissues samples, however, relatively lower accuracy for boold platelets samples.

     

国人睾丸、附睾和输精管的水解酶的组织化学观察

本文报导国人睾丸、附睾和输精管的ＮＳＥ,ＡＣｈＥ,ＣｈＥ,ＡＬＰ,ＡＣＰ,５＇－Ｎａｓｅ,Ｇ－６－Ｐａｓｅ,β－ＧＡ,β－ＧＲ,ＡＰ－Ｍ,ＡＴＰａｓｅ和ＴＰＰａｓｅ水解酶的组织化学活性、结果显示：睾丸曲细精管的ＡＬＰ,５＇－Ｎａｓｅ和ＡＴＰａｓｅ;睾丸间质细胞的ＮＳＥ,ＡＬＰ,ＡＴＰａｓｅ和ＡＣＰ;睾丸间质中的ＮＳＥ,ＡＬＰ和ＡＴ－Ｐａｓｃ;睾丸输出小管和附睾管上皮的ＮＳＥ,ＡＬＰ,ＡＣＰ,５’－Ｎａｓｅ,β－ＧＡ,β－ＧＲ,ＡＴＰａｓｅ和Ｔｐｐａｓｅ;附睾头部间质中的ＮＳＥ,ＡＣｈＥ,ＡＬＰ,和ＡＴＰａｓｅ;输精管上皮细胞的ＡＴＰａｓｅ的酶活性均呈强阳性或极强阳性。说明人类睾丸、附睾和输精管含有丰富的水解酶,尤其是附睾头部的输出小管、附睾管和头质均含有种类多活性高的水解酶,在精子的功能成熟上起了重要的作用,提示其可能作为生育与不育诊治中的重要指标。     

螺旋对称病毒衣壳参数的研究

本文从数学角度分析和研究了螺旋对称病毒衣壳参数、整理出衣壳参数２０多个,对每一个参数的概念、含义等给予了明确的认定。提示了参数间的关系,推导出了一些计算参数值的公式。     

New formulae for folding catalysts make them multi-purpose enzymes

Whereas protein disulfide isomerase (PDI) and prolyl isomerase (PPI) are considered as efficient protein folding catalysts, very few large scale processes use them because of economical and technical limitations. PDI and PPI were successfully immobilized on cross-linked agarose beads. PDI inactivation during coupling reaction was overcome by oxidizing active site thiols with dimethylsulfoxide and led to a 64% active enzyme. Alternatively, PPI and PDI biotinylation resulted in 100% and 55-66% active enzymes respectively. The use of these modified catalysts suppresses post-refolding purification and enables the design of biochemical reactors. Several other possible applications are also discussed. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 645-649, 1997.     

福腮钩土蜂生物学及其利用的研究

福腮钩土蜂是大黑鳃金龟幼虫的一种外寄生天敌。成蜂以红麻、甘薯蜜腺和菜豆花蜜为补充营养,卵主要产于寄主后胸与第一腹节之间的腹面．单雌平均产卵22粒。幼虫共4龄,咀食寄主组织,只残留头壳,老熟幼虫作茧越冬。生活史有1年1代和2年1代型,成蜂发生时期与大黑鳃金龟发生期相一致。据此提出,在花生田种植蜜源植物,为土蜂提供食物资源．通过从蜂源地助迁土蜂已在邹城市定居．展示有明显的自然控制作用。     

Cystic Fibrosis: A Disease of Altered Protein Folding

Cystic fibrosis (CF) is caused by mutations in the gene that encodes the cystic fibrosis transmembrane conductance regulator, CFTR. Previously we demonstrated that the common F508 mutation in the first nucleotide binding domain (NBD1) alters the ability of the domain to fold into a functional three-dimensional structure, providing a molecular explanation for the observation that the mutant CFTR is retained in the endoplasmic reticulum and does not traffic to the apical membrane of affected epithelial cells. Notably, when conditions are altered to promote folding of the mutant protein, it can assume a functional conformation. Correcting the folding defect may have therapeutic benefit for the treatment of cystic fibrosis. Here we summarize these results and discuss the implications in vitro folding studies have for understanding the pathobiology of CF.     

Determination of serotonin, catecholamines and their metabolites by direct injection of supernatants from chicken brain tissue homogenate using liquid chromatography with electrochemical detection

An isocratic liquid chromatographic method with electrochemical detection for the determination of

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-3,4-dihydroxyphenylalanine, dopamine, norepinephrine, epinephrine, serotonin, and their major metabolites, 3,4-dihydroxyphenylacetic acid, 4-hydroxy-3-methoxyphenylacetic acid and 5-hydroxyindole-3-acetic acid in chicken brain tissue is described. Chickens were killed at different ages, the brains were quickly frozen and 300-μm cryostat sections were made. From these sections, two to six tissue micropunches (1 mm in diameter) were punched out from 20 different areas of the hypothalamus and homogenated in 100 μl 0.1 M perchloric acid which included 0.01% cysteine as antioxidant. Fifty-μl supernatants were injected directly onto the LC system, separated on a 3-μm Phase II ODS column (100×3.2 mm I.D.) and detected by an electrochemical detector at a potential of +0.75 V. Standard curves, recoveries, analytical precision and detection limits were investigated for each monoamine neurotransmitter and its metabolites. The method was applied to study the influence of food restriction on the concentration of monoamine neurotransmitters in different brain areas, known to be involved in feeding and reproductive behaviour of female broiler chickens. Over 1000 micropunched tissue samples from ad libitum fed and food-restricted female broiler chickens were analyzed. Our results provide a possible role for catecholamines and indolamines in the altered feeding and reproductive behaviour of the broiler chicken.     

海水中Cu、Zn离子对牟氏角毛藻生长的生态效应

研究了Ｃｕ、Ｚｎ离子对车氏角毛藻生长的生态效应．结果表明,Ｃｕ离子活度低于１０－７．８０ｍｏｌ·Ｌ－１时,角毛藻生长繁殖良好,其中以１０－１３．５７～１０－１０．５２ｍｏｌ·Ｌ－１为最好;Ｃｕ离子活度≥１０－７．８０ｍｏｌ·Ｌ－１时产生毒性．低Ｚｎ离子活度未表现出对车氏角毛藻的必需性,Ｚｎ离子活度＞１０－７．００ｍｏｌ·Ｌ－１时不利于生长繁殖．与Ｚｎ离子相比,牟氏角毛藻对Ｃｕ离子的毒性更为敏感．     

Visualisation of capillaries in human skeletal muscle

 A double staining method combining Ulex europaeus agglutinin I lectin (UEA-I) and collagen type IV staining was used to determine the capillary density and the number of capillaries relative to different fibre types in human skeletal muscles. The result of this combined staining was compared with that of other staining methods including amylase-periodic acid Schiff (PAS), UEA-I, anti-collagen type IV and anti-von Willebrand factor. Muscle biopsy specimens, 12 from M. vastus lateralis and 6 from M. soleus, were obtained from 18 healthy young men. Compared with amylase-PAS staining, double staining showed a larger number of capillaries surrounding type I (+9.6%), type IIA (+8.6%) and type IIB (+11.6%) fibres in the M. vastus lateralis specimens (P<0.001 for all differences). The capillary to fibre ratio (cap·fibre^–1) and the capillary density (cap·mm^–2) were 8.3% (P<0.002) and 7.9% (P<0.001) larger, respectively. In the M. soleus specimens, cap·fibre^–1 and cap·mm^–2 were 7.4 and 9.9% larger, respectively, by double staining compared with PAS staining. Further comparisons showed that the cap·fibre^–1 and cap·mm^–2 obtained with double staining were similar to the values determined by the UEA-I staining, but greater than that measured by the collagen type IV method. The double staining gave a more marked stain of capillaries and revealed muscle fibre borders clearly, which is an advantage in studies that require comparisons between serial sections using computerised image analyses. It is concluded that the double staining method is superior to either the UEA-I, collagen type IV or the traditional amylase-PAS staining methods in analysing capillary density of normal human skeletal muscle. Accepted: 17 October 1996